Meta-omics integration approach reveals the effect of soil native microbiome diversity in the performance of inoculant Azospirillum brasilense

Abstract

Plant growth promoting bacteria (PGPB) have been used as integrative inputs to minimize the use of chemical fertilizers. However, a holistic comprehension about PGPB-plant-microbiome interactions is still incipient. Furthermore, the interaction among PGPB and the holobiont (host-microbiome association) represent a new frontier to plant breeding programs. We aimed to characterize maize bulk soil and rhizosphere microbiomes in irradiated soil (IS) and a native soil (NS) microbial community gradient (dilution-to-extinction) with Azospirillum brasilense Ab-V5, a PGPB commercial inoculant. Our hypothesis was that plant growth promotion efficiency is a result of PGPB niche occupation and persistence according to the holobiont conditions. The effects of Ab-V5 and NS microbial communities were evaluated in microcosms by a combined approach of microbiomics (species-specific qPCR, 16S rRNA metataxonomics and metagenomics) and plant phenomics (conventional and high-throughput methods). Our results revealed a weak maize growth promoting effect of Ab-V5 inoculation in undiluted NS, contrasting the positive effects of NS dilutions 10−3, 10−6, 10−9 and IS with Ab-V5. Alpha diversity in NS + Ab-V5 soil samples was higher than in all other treatments in a time course of 25 days after sowing (DAS). At 15 DAS, alpha diversity indexes were different between NS and IS, but similar in all NS dilutions in rhizospheric samples. These differences were not persistent at 25 DAS, demonstrating a stabilization process in the rhizobiomes. In NS 10−3 +Ab-V5 and NS 10−6 Ab-V5, Ab-V5 persisted in the maize rhizosphere until 15 DAS in higher abundances compared to NS. In NS + Ab-V5, abundance of six taxa were positively correlated with response to (a)biotic stresses in plant-soil interface. Genes involved in bacterial metabolism of riboses and amino acids, and cresol degradation were abundant on NS 10−3 + Ab-V5, indicating that these pathways can contribute to plant growth promotion and might be a result of Ab-V5 performance as a microbial recruiter of beneficial functions to the plant. Our results demonstrated the effects of holobiont on Ab-V5 performance. The meta-omics integration supported by plant phenomics opens new perspectives to better understanding of inoculants-holobiont interaction and for developing better strategies for optimization in the use of microbial products.

Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly

“…Such research has shed light on changes in soil microbial communities under biotic disturbances [ 87 ]. For example, Ferrarezi et al [ 88 ] demonstrated that the PGPR Azospirillum brasilense had a more pronounced beneficial impact on plants growing in soils with lower microbial diversity, as determined by applying the dilution-to-extinction method. It is important to emphasize that the autoclaved soil did not receive any microbial inoculum, and the microbial communities found in this treatment originated naturally from the soil.…”

The Effectiveness of Co-Inoculation by Consortia of Microorganisms Depends on the Type of Plant and the Soil Microbiome

“…In this regard, an increase in alpha diversity is often associated with better soil productivity, since a variety of microorganisms provide nutrition and protect the plant from stress in different conditions [ 20 ]. However, it was shown that a decrease in the alpha diversity of the soil before the inoculation of Azospirillum brasilense reduced interspecific microbial competition and triggered the processes of the recolonization of plants by bacteria associated with PGPB effects [ 21 ]. The species richness of the soil microbial community (alpha diversity) was similar for all studied samples.…”

The recent genetic modification techniques for improve soil conservation, nutrient uptake and utilization

“… 127–129 Moreover, gene function prediction and the creation of customized genetic modifications for particular agronomic traits are made easier by the combination of bioinformatics and computational modeling. 128 , 130 , 131 Future GM technologies will be used to create highly productive and sustainable crop varieties that maximize nutrient uptake, conserve soil, and raise total agricultural yield.…”